Editing LiteMol:Hierarchy (section)

=Structures=

This section describes the entities used for representation of molecular models and electron density maps. It does not contain any information about how these data are visualized.

==Root Entity==

The highest level of the hierarchy is the '''Root Entity''', which is created at the beginning of LiteMol session. It represents the starting point of all actions and all other entities you create are its direct or indirect descendants.

Applicable actions:
* '''Molecule''' – Loads a structure of a molecule and creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity. The structure can be obtained from several sources:
** '''CoordinateServer''' - Downloads the structure from an internet location that provides [https://webchem.ncbr.muni.cz/CoordinateServer CoordinateServer] functionality. These parameters can be set: 
*** '''Id''' - Specify the PDB identifier of the structure.
*** '''Type''' - Can be either '''Full''' (coordinates of all atoms are downloaded) or '''Cartoon''' (only atoms necessary for cartoon visualization are downloaded, so the download will be faster).
*** '''Low Precision''' - If '''Low Precision''' = Off, the atomic coordinates are downloaded in full precision (3 decimal places). If '''Low Precision''' = On, then the coordinates are downloaded only with 1 decimal place. This change is almost unnoticeable in the visualized structure but less data are downloaded.
*** '''Server''' - By default, the data are downloaded from the CoordinateServer located at webchem.ncbr.muni.cz/CoordinateServer, however, this can be changed.
** '''PDBe Updated mmCIF''' - Downloads the structure from the PDBe server (e.g. www.ebi.ac.uk/pdbe/static/entry/1cbs_updated.cif) using the updated mmCIF format file. 
** '''URL''' - Downloads the structure from any specified internet location.
** '''File on Disk''' - Loads the structure from a file on your computer. The format of the file will be inferred from its extension.
* '''Density Data from PDBe''' – Downloads the electron density or electronic potential map for a molecule specified by its PDB ID (or EMDB ID) from the PDBe server and creates a [[LiteMol:Hierarchy#Density Data (DD) | Density Data]] entity. However, a much faster way to visualize densities is to create a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity and then use the '''Density Streaming''' action. 
* '''Coordinate Streaming''' – Downloads the portion of structural data that is necessary for simple visualization of a molecule. If more data are needed later, they will be downloaded automatically. This behavior is particularly useful when working with extremely large molecules, where full download may take more time, or when limited by hardware resources (slow/expensive Internet connection, limited memory) especially on mobile devices. You can specify what server should be used as the source of the data (e.g. http://webchemdev.ncbr.muni.cz/CoordinateServer or http://www.ebi.ac.uk/pdbe/coordinates). Creates a [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity.
* '''Download Data''' - Acquires a data file from a URL. The type of the file must be specified in advance (String (textual encoding) or Binary). Creates a [[LiteMol:Hierarchy#String Data (SD) | String Data]] or a [[LiteMol:Hierarchy#Binary Data (BD) | Binary Data]] entity.
* '''Open Data File''' - Loads a data file from your computer. The type of the file must be specified in advance (String (textual encoding) or Binary). Creates a [[LiteMol:Hierarchy#String Data (SD) | String Data]] or a [[LiteMol:Hierarchy#Binary Data (BD) | Binary Data]] entity.


==Molecule (M)==

A '''Molecule''' entity represents a set of structural data for a '''Molecule''' (which corresponds to one PDB entry or one mmCIF file).

Applicable actions:
* '''Model''' – Creates a model of the molecule ([[LiteMol:Hierarchy#Molecule Model (MM) |Molecule Model]] entity). Some PDB entries (mostly NMR structures) contain multiple models, in such case, the sequential number ('''Index''') of the desired model to be displayed can be specified.
* '''Density Streaming''' - Creates a [[LiteMol:Hierarchy#Density Streaming (BDS) |Density Streaming]] for this molecule. Clicking on an atom or residue in the structure will instantly download and display the density data for the surrounding region. This solution is, in general, much faster than downloading the whole density map (often more than 1 GB). More details are available [http://webchem.ncbr.muni.cz/DensityServer here].
* '''PDBe Validation Report''' – Downloads wwPDB validation data for this molecule from PDBe and creates a [[LiteMol:Hierarchy#Validation Report (VR) |Validation Report]] entity.
* '''Ligand Validation Report''' - Downloads validation data for the ligands in this molecule from [http://webchem.ncbr.muni.cz/Platform/ValidatorDb ValidatorDB] and creates a [[LiteMol:Hierarchy#Validation Report (VR) |Validation Report]] entity.
* '''PDBe Sequence Annotations''' – Downloads sequence annotation data for this molecule from PDBe (collected from sources such as UniProt, InterProt, Pfam etc.) and creates a [[LiteMol:Hierarchy#Sequence Annotations (SA) | Sequence Annotations]] entity.

==Molecule Model (M<sub>M</sub>)==

[[File:LiteMol-default.png | thumb | 400px | right| Model of the protein with PDB identifier 1CBS in default visualization produced by '''Macromolecule Visual''' ('''Cartoon''' for biopolymer, '''Balls and Sticks''' for non-biopolymer ligand, and '''Balls and sticks''' with '''Opacity''' 0.25 for water molecules). ]]

A '''Molecule Model''' entity represents a static model of a molecule, i.e. 3D coordinates of each atom. (If your PDB entry contains multiple alternative models, each of them will be in a separate '''Molecule Model''' entity.)

Applicable actions:
* '''Selection''' – Selects a part of the model and creates [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Molecule Model Selection]] entity. Selections are defined using [[LiteMol:SelectionAlgebra | selection algebra language]].
* '''Assembly''' – Some PDB entries contain information about how multiple copies of the molecule should be positioned in space in order to create an assembly (e.g. a virus capsid). Alternatively,  just a part of the model can constitute a relevant assembly (e.g. the model contains a two molecules while a monomer is present ''in vivo''). This action applies this information to your model and creates a new model containing the assembly. Some PDB entries provide more than one assembly.
* '''Crystal Symmetry''' – Creates a new model containing the original molecule and its closest neighbours in the crystal structure. Two modes are available: '''Interaction''' shows only those atoms that are within the specified radius (in Angstrom) from the original structure, '''Mates''' shows all copies of the structure that have at least one atom within this radius. This action is obviously not available for structures determined by NMR.
* '''Macromolecule Visual''' – Creates a visual representation of the model. If the model contains several types of molecules (e.g. protein + ligand), these are organized in a group of selections and appropriate visualization is used for each selection (e.g. '''Cartoon''' for protein but '''Balls and sticks''' for ligand). The same visuals are created automatically when the '''Molecule Model''' entity is created.
* '''Visual''' – Creates a visual representation of the model. This option is less automatic than '''Macromolecule Visual''' but more flexible. Type, coloring, and other attributes of the created [[LiteMol:Hierarchy#Molecule Visual (VM) | Visual]] can be specified. Find more about these settings [[LiteMol:Hierarchy#Molecule Visual (VM) | here]].
* '''Coordinate Streaming''' – Works in a similar way as '''Coordinate Streaming''' from the [[LiteMol:Hierarchy#Root Entity | Root Entity]]. If you click on an atom or residue, the coordinates of all atoms in the surrounding volume will be downloaded instantly. This can be useful when a part of the structure has already been downloaded (e.g. the protein backbone) and some additional atoms are required (e.g. sidechains to display the binding site).
* '''Update Model''' – Applicable when multiple models are included in the PDB entry (typical case for NMR structures). This action will remove the current model and create a new model with the specified index (model number). Please keep in mind that this will remove all the changes you have applied to the current model! If you don't want to loose these changes, go to the superior [[LiteMol:Hierarchy#Molecule (M) | Molecule]] entity and create a new model in addition to the current model.


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==Group (G)==

This type of entity is used to organize multiple entities that are logically connected. For example, a group of selections containing different parts of a model (protein, ligand, and water) or a group of sequence annotations obtained from the same database.

==Molecule Model Selection (S<sub>M</sub>)==

This is an entity representing a subset of a molecule model. An example is one protein chain, one atom, or a set of all alanine residues. A selection can be created from either a [[LiteMol:Hierarchy#Molecule Model (MM) | Molecule Model]] entity or a [[LiteMol:Hierarchy#Molecule Visual (VM) | Molecule Visual]] entity. Selections are created using [[LiteMol:SelectionAlgebra | selection algebra language]].

Applicable actions:
* '''Visual''' – Create a visual representation of this selection. Type, coloring, and other attributes of the created [[LiteMol:Hierarchy#Molecule Visual (VM) | Visual]] can be specified. Find more about these settings [[LiteMol:Hierarchy#Molecule Visual (VM) | here]].
* '''Update Selection''' - Change the name of the [[LiteMol:Hierarchy#Molecule Model Selection (SM) | Selection]] or change its definition using [[LiteMol:SelectionAlgebra | selection algebra language]]. (This action may not be not available for automatically generated selections.)

==Density Data (DD)==

Represents a three-dimensional map of electron density (for X-ray crystal structures) or electronic potential maps (for cryo-EM structures). Two types of maps are available for most crystal structures where structure factors are available in the PDB archive: '''2Fo-Fc''' and '''Fo-Fc'''.

Applicable actions:
* '''Surface''' – Creates a visualization of the density isosurface with the defined isovalue ([[LiteMol:Hierarchy#Density Visual (VDD) |Density Visual]] entity).
* '''Interactive Surface''' – Creates a density isosurface which is shown only for a region of the molecule when you click on that region ([[LiteMol:Hierarchy#Interactive Surface (BIS) |Interactive Surface]] entity).
* '''Update CCP4/Map''' – Allows you to see the properties of this density map, such as standard deviation, minimum, maximum, and mean value.